{"action":"created","issue":{"url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/6449","repository_url":"https://api.github.com/repos/Homebrew/homebrew-science","labels_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/6449/labels{/name}","comments_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/6449/comments","events_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/6449/events","html_url":"https://github.com/Homebrew/homebrew-science/issues/6449","id":273430645,"number":6449,"title":"Issue installing GATK ","user":{"login":"biomendi","id":12748102,"avatar_url":"https://avatars2.githubusercontent.com/u/12748102?v=4","gravatar_id":"","url":"https://api.github.com/users/biomendi","html_url":"https://github.com/biomendi","followers_url":"https://api.github.com/users/biomendi/followers","following_url":"https://api.github.com/users/biomendi/following{/other_user}","gists_url":"https://api.github.com/users/biomendi/gists{/gist_id}","starred_url":"https://api.github.com/users/biomendi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/biomendi/subscriptions","organizations_url":"https://api.github.com/users/biomendi/orgs","repos_url":"https://api.github.com/users/biomendi/repos","events_url":"https://api.github.com/users/biomendi/events{/privacy}","received_events_url":"https://api.github.com/users/biomendi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2017-11-13T13:33:32Z","updated_at":"2017-11-13T13:38:53Z","closed_at":null,"author_association":"NONE","body":"### Indicate troubleshooting steps taken\r\n\r\n- [ Yes ] Ran `brew update` and retried your prior step?\r\n- [ Yes ] Ran `brew doctor`, fixed as many issues as possible and retried your prior step?\r\n- [ No ] Checked that a similar issue hasn't already been filed?\r\n- [ No ] Looked up the software bug tracker if reporting a build error?\r\n- [ No ] If you're seeing permission errors tried running `sudo chown -R $(whoami) $(brew --prefix)`?\r\n\r\n### Bug reports / build errors:\r\n\r\n#### Brief summary of issue:\r\n\r\n$ brew install gatk\r\n\r\nUpdating Homebrew...\r\n==> Auto-updated Homebrew!\r\nUpdated 2 taps (caskroom/cask, homebrew/core).\r\n==> Updated Formulae\r\nbchunk                               faas-cli                             grafana                              itstool\r\n\r\n==> Installing gatk from homebrew/science\r\n==> Downloading https://github.com/broadgsa/gatk-protected/archive/3.6.tar.gz\r\nAlready downloaded: /Users/server_mac1/Library/Caches/Homebrew/gatk-3.6.tar.gz\r\n==> mvn package -Dmaven.repo.local=${PWD}/repo\r\nLast 15 lines from /Users/server_mac1/Library/Logs/Homebrew/gatk/01.mvn:\r\n\tat java.net.URLClassLoader.defineClass(URLClassLoader.java:283)\r\n\tat java.net.URLClassLoader.access$000(URLClassLoader.java:58)\r\n\tat java.net.URLClassLoader$1.run(URLClassLoader.java:197)\r\n\tat java.security.AccessController.doPrivileged(Native Method)\r\n\tat java.net.URLClassLoader.findClass(URLClassLoader.java:190)\r\n\tat org.codehaus.plexus.classworlds.realm.ClassRealm.loadClassFromSelf(ClassRealm.java:401)\r\n\tat org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy.loadClass(SelfFirstStrategy.java:42)\r\n\tat org.codehaus.plexus.classworlds.realm.ClassRealm.unsynchronizedLoadClass(ClassRealm.java:271)\r\n\tat org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:254)\r\n\tat org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:239)\r\n\tat org.codehaus.plexus.classworlds.launcher.Launcher.getMainClass(Launcher.java:144)\r\n\tat org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:266)\r\n\tat org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)\r\n\tat org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)\r\n\tat org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)\r\n\r\nREAD THIS: https://docs.brew.sh/Troubleshooting.html\r\n\r\n\r\n#### The complete command that you issued: \r\n\r\nbrew install gatk\r\n\r\n#### Gist with output of `brew doctor`:\r\n\r\nYour system is ready to brew.\r\n\r\n#### Link output by `brew gist-logs <formula>`:\r\n\r\nhttps://gist.github.com/68499adb844116ffcf7e0cfffde1a243\r\n\r\n#### Output of `brew config`:\r\n\r\nHOMEBREW_VERSION: 1.3.7\r\nORIGIN: https://github.com/Homebrew/brew\r\nHEAD: 441c212f2dd70f053ee21eac8398c5fe5dfd0551\r\nLast commit: 3 days ago\r\nCore tap ORIGIN: https://github.com/Homebrew/homebrew-core\r\nCore tap HEAD: 0d9b9d4f1cfbef8a7a271ceecddad2a52eea1a55\r\nCore tap last commit: 7 minutes ago\r\nHOMEBREW_PREFIX: /usr/local\r\nHOMEBREW_GIT_CONFIG_FILE: /usr/local/Homebrew/.git/config\r\nCPU: 24-core 64-bit arrandale\r\nHomebrew Ruby: 2.3.3 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.3/bin/ruby\r\nClang: 9.0 build 900\r\nGit: 2.13.6 => /Applications/Xcode.app/Contents/Developer/usr/bin/git\r\nCurl: 7.54.0 => /usr/bin/curl\r\nPerl: /usr/bin/perl\r\nPython: /usr/bin/python\r\nRuby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby\r\nJava: 9.0.1, 1.6.0_65-b14-468\r\nmacOS: 10.12.6-x86_64\r\nXcode: 9.1\r\nCLT: 9.0.1.0.1.1506734476\r\nX11: N/A\r\n\r\n### Formula Requests: NO\r\n\r\n**The quickest way to get a new formula into Homebrew is to file a [Pull Request](https://github.com/Homebrew/homebrew-science/pulls)**.\r\n\r\nWe will consider your request but it may be closed if it's something we're not actively planning to work on.\r\n"},"comment":{"url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/comments/343921231","html_url":"https://github.com/Homebrew/homebrew-science/issues/6449#issuecomment-343921231","issue_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/6449","id":343921231,"user":{"login":"ilovezfs","id":5268928,"avatar_url":"https://avatars2.githubusercontent.com/u/5268928?v=4","gravatar_id":"","url":"https://api.github.com/users/ilovezfs","html_url":"https://github.com/ilovezfs","followers_url":"https://api.github.com/users/ilovezfs/followers","following_url":"https://api.github.com/users/ilovezfs/following{/other_user}","gists_url":"https://api.github.com/users/ilovezfs/gists{/gist_id}","starred_url":"https://api.github.com/users/ilovezfs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ilovezfs/subscriptions","organizations_url":"https://api.github.com/users/ilovezfs/orgs","repos_url":"https://api.github.com/users/ilovezfs/repos","events_url":"https://api.github.com/users/ilovezfs/events{/privacy}","received_events_url":"https://api.github.com/users/ilovezfs/received_events","type":"User","site_admin":false},"created_at":"2017-11-13T13:38:53Z","updated_at":"2017-11-13T13:38:53Z","author_association":"OWNER","body":"I see this doesn't have any bottles … that same change will have to be made in the formula unfortunately."}}
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